A Heuristic Algorithm for Individual Haplotyping with Minimum Error Correction. - Abdullah Al Mueen; Md. Shamsuzzoha Bayzid; Md. Maksudul Alam; Md. Saidur Rahman 001 (BMEI (1), 2008)

Discovering Pairwise Compatibility Graphs. - Muhammad Nur Yanhaona; Md. Shamsuzzoha Bayzid; Md. Saidur Rahman 001 (Discret. Math. Algorithms Appl., 2010)

Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence. - Md. Shamsuzzoha Bayzid; Tandy J. Warnow (J. Comput. Biol., 2012)

Inferring Optimal Species Trees Under Gene Duplication and Loss. - Md. Shamsuzzoha Bayzid; Siavash Mirarab; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2013)

Naive binning improves phylogenomic analyses. - Md. Shamsuzzoha Bayzid; Tandy J. Warnow (Bioinform., 2013)

ASTRAL: genome-scale coalescent-based species tree estimation. - Siavash Mirarab; Rezwana Reaz; Md. Shamsuzzoha Bayzid; Théo Zimmermann; M. Shel Swenson; Tandy J. Warnow (Bioinform., 2014)

Gene Tree Parsimony for Incomplete Gene Trees. - Md. Shamsuzzoha Bayzid; Tandy J. Warnow (WABI, 2017)

Gene tree parsimony for incomplete gene trees: addressing true biological loss. - Md. Shamsuzzoha Bayzid; Tandy J. Warnow (Algorithms Mol. Biol., 2018)

A 'phylogeny-aware' multi-objective optimization approach for computing MSA. - Muhammad Ali Nayeem; Md. Shamsuzzoha Bayzid; Atif Hasan Rahman 001; Rifat Shahriyar; M. Sohel Rahman (GECCO, 2019)

A Multi-objective Metaheuristic Approach for Accurate Species Tree Estimation. - Muhammad Ali Nayeem; Md. Shamsuzzoha Bayzid; Sakshar Chakravarty; Mohammad Saifur Rahman 001; M. Sohel Rahman (BIBE, 2020)

SAINT: self-attention augmented inception-inside-inception network improves protein secondary structure prediction. - Mostofa Rafid Uddin; Sazan Mahbub; Mohammad Saifur Rahman 001; Md. Shamsuzzoha Bayzid (Bioinform., 2020)

Align-gram : Rethinking the Skip-gram Model for Protein Sequence Analysis. - Nabil Ibtehaz; S. M. Shakhawat Hossain Sourav; Md. Shamsuzzoha Bayzid; M. Sohel Rahman (CoRR, 2020)

3D-FFS: Faster 3D object detection with Focused Frustum Search in sensor fusion based networks. - Aniruddha Ganguly; Tasin Ishmam; Khandker Aftarul Islam; Md Zahidur Rahman; Md. Shamsuzzoha Bayzid (IROS, 2021)

Biological computation and computational biology: survey, challenges, and discussion. - Zaineb Chelly Dagdia; Pavel Avdeyev; Md. Shamsuzzoha Bayzid (Artif. Intell. Rev., 2021)

SSG-LUGIA: Single Sequence based Genome Level Unsupervised Genomic Island Prediction Algorithm. - Nabil Ibtehaz; Ishtiaque Ahmed; Md. Sabbir Ahmed; M. Sohel Rahman; Rajeev K. Azad; Md. Shamsuzzoha Bayzid (Briefings Bioinform., 2021)

wQFM: highly accurate genome-scale species tree estimation from weighted quartets. - Mahim Mahbub; Zahin Wahab; Rezwana Reaz; Mohammad Saifur Rahman 001; Md. Shamsuzzoha Bayzid (Bioinform., 2021)

QT-GILD: Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data. - Sazan Mahbub; Shashata Sawmya; Arpita Saha; Rezwana Reaz; M. Sohel Rahman; Md. Shamsuzzoha Bayzid (RECOMB, 2022)

Fast and Accurate Branch Support Calculation for Distance-Based Phylogenetic Placements. - Navid Bin Hasan; Avijit Biswas; Metin Balaban; Siavash Mirarab; Md. Shamsuzzoha Bayzid (RECOMB-CG, 2022)

EGRET: edge aggregated graph attention networks and transfer learning improve protein-protein interaction site prediction. - Sazan Mahbub; Md. Shamsuzzoha Bayzid (Briefings Bioinform., 2022)

PASTA with many application-aware optimization criteria for alignment based phylogeny inference. - Muhammad Ali Nayeem; Md. Shamsuzzoha Bayzid; Naser Anjum Samudro; Mohammad Saifur Rahman 001; M. Sohel Rahman (Comput. Biol. Chem., 2022)

Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data. - Sazan Mahbub; Shashata Sawmya; Arpita Saha; Rezwana Reaz; M. Sohel Rahman; Md. Shamsuzzoha Bayzid (J. Comput. Biol., 2022)

Multiobjective Formulation of Multiple Sequence Alignment for Phylogeny Inference. - Muhammad Ali Nayeem; Md. Shamsuzzoha Bayzid; Atif Hasan Rahman 001; Rifat Shahriyar; M. Sohel Rahman (IEEE Trans. Cybern., 2022)

CD-MAWS: An Alignment-Free Phylogeny Estimation Method Using Cosine Distance on Minimal Absent Word Sets. - Naser Anjum; Raian Latif Nabil; Rakibul Islam Rafi; Md. Shamsuzzoha Bayzid; Mohammad Saifur Rahman 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Inferring Optimal Species Trees in the Presence of Gene Duplication and Loss: Beyond Rooted Gene Trees. - Md. Shamsuzzoha Bayzid (J. Comput. Biol., 2023)

BEENE: deep learning-based nonlinear embedding improves batch effect estimation. - Md Ashiqur Rahman; Abdullah Aman Tutul; Mahfuza Sharmin; Md. Shamsuzzoha Bayzid (Bioinform., 2023)

Gene Tree Parsimony in the Presence of Gene Duplication, Loss, and Incomplete Lineage Sorting. - Prottoy Saha; Md Shamiul Islam; Tasnim Rahman; Adiba Shaira; Kazi Noshin; Rezwana Reaz; Md. Shamsuzzoha Bayzid (RECOMB-CG, 2024)

An alignment-free method for phylogeny estimation using maximum likelihood. - Tasfia Zahin; Md. Hasin Abrar; Mizanur Rahman Jewel; Tahrina Tasnim; Md. Shamsuzzoha Bayzid; Atif Rahman 001 (BMC Bioinform., 2025)